The mid-winter is set to be bleaker for millions of rail travellers as inflation-busting fare rises take effect.

Regulated fares, which include season tickets, are increasing by an average of 4.2%, with the overall average rise for all tickets being 3.9%.

The rise follows a miserable few weeks for many commuters who have had to contend with floods, signal failures and, on some routes, staff shortages. Last week, over-running engineering work led to serious over-crowding on some trains.

Campaign groups have pointed out the latest increase is the 10th successive above-inflation rise, with some rail season ticket holders seeing their fares rise by more than 50% in the last 10 years. Also, the TUC has said that fares have risen far faster than wages since the recession in 2008.

Train companies can put some season tickets up by more than 4.2% as long as the overall average does not exceed 4.2%. So, for example, a Leeds to Wakefield season ticket is rising 6.16%, while a Ludlow to Hereford season ticket is increasing 5.28%. Some Kent commuters are also facing above-average rises, with season tickets to London from Ramsgate, Folkestone, Canterbury, Deal and Dover all going up by around 4.8%.

Some travellers will escape the worst of the increases. Those commuting to London from Aylesbury in Buckinghamshire, for example, will only have to pay 3.18% more for their season tickets.

The Association of Train Operating Companies (Atoc) said it recognised nobody liked paying more for their journey. But it added that railway funding could only come from taxpayers or from passengers "and the Government's policy remains that a bigger share must come from people who use the train".

Transport Minister Norman Baker said the Government had reduced fare rises planned for January 2013 and January 2014 from RPI plus 3% to RPI plus 1%.

He added: "We are engaged in the biggest rail investment programme since the 19th century and it is only right that the passenger, as well as the taxpayer, contributes towards that. In the longer term, we are determined to reduce the cost of running the railways so that we can end the era of above-inflation fare rises."

Labour highlighted the fact that some season tickets are allowed to rise by more than the 4.2% average. Shadow transport secretary Maria Eagle said: "David Cameron misled commuters when he promised to cap fare rises at 1% above inflation. The Government should come clean with commuters that this is a direct result of their decision to cave in to pressure from the private train companies to let them hike ticket prices beyond the so-called cap."